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Research Article

m6A Rna Modification Modulates Gene Expression and Cancer-Related Pathways in Clear Cell Renal Cell Carcinoma

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Pages 87-99 | Received 03 Jul 2019, Accepted 28 Nov 2019, Published online: 20 Dec 2019

References

  • Dominissini D , Moshitch-MoshkovitzS , SchwartzSet al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature485(7397), 201–206 (2012).
  • Wang Y , LiY , TothJI , PetroskiMD , ZhangZ , ZhaoJC. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat. Cell Biol.16(2), 191–198 (2014).
  • Wang X , LuZ , GomezAet al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature505(7481), 117–120 (2014).
  • Wang X , ZhaoBS , RoundtreeIAet al. N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell161(6), 1388–1399 (2015).
  • Alarcon CR , LeeH , GoodarziH , HalbergN , TavazoieSF. N6-methyladenosine marks primary microRNAs for processing. Nature519(7544), 482–485 (2015).
  • Xiang Y , LaurentB , HsuCHet al. RNA m(6)A methylation regulates the ultraviolet-induced DNA damage response. Nature543(7646), 573–576 (2017).
  • Fu Y , DominissiniD , RechaviG , HeC. Gene expression regulation mediated through reversible m(6)A RNA methylation. Nat. Rev. Genet.15(5), 293–306 (2014).
  • Deng X , SuR , WengH , HuangH , LiZ , ChenJ. RNA N(6)-methyladenosine modification in cancers: current status and perspectives. Cell Res.28(5), 507–517 (2018).
  • Liu J , EckertMA , HaradaBTet al. m(6)A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat. Cell Biol.20(9), 1074–1083 (2018).
  • Chen M , WeiL , LawCTet al. RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2. Hepatology67(6), 2254–2270 (2018).
  • Zhang S , ZhaoBS , ZhouAet al. m(6)A demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer cell31(4), 591.e6–606.e6 (2017).
  • Li Z , WengH , SuRet al. FTO plays an oncogenic role in acute myeloid leukemia as a N(6)-methyladenosine RNA demethylase. Cancer Cell31(1), 127–141 (2017).
  • Meyer KD , SaletoreY , ZumboP , ElementoO , MasonCE , JaffreySR. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell149(7), 1635–1646 (2012).
  • Frew IJ , MochH. A clearer view of the molecular complexity of clear cell renal cell carcinoma. Annu. Rev. Pathol.10, 263–289 (2015).
  • Martin M . Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J.17(1), 10–12 (2011).
  • Kim D , LangmeadB , SalzbergSL. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods12(4), 357–360 (2015).
  • Zhang Y , LiuT , MeyerCAet al. Model-based analysis of ChIP-Seq (MACS). Genome Biol.9(9), R137 (2008).
  • Shen L , ShaoNY , LiuX , MazeI , FengJ , NestlerEJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS ONE8(6), e65598 (2013).
  • Alexa A , RahnenführerJ. Gene set enrichment analysis with topGO (2009). https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
  • Tian L , GreenbergSA , KongSW , AltschulerJ , KohaneIS , ParkPJ. Discovering statistically significant pathways in expression profiling studies. Proc. Natl Acad. Sci. USA102(38), 13544–13549 (2005).
  • Chen T , HaoYJ , ZhangYet al. m(6)A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell16(3), 289–301 (2015).
  • Thorvaldsdottir H , RobinsonJT , MesirovJP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform.14(2), 178–192 (2013).
  • Shannon P , MarkielA , OzierOet al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res.13(11), 2498–2504 (2003).
  • Tang Z , LiC , KangB , GaoG , LiC , ZhangZ. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res.45(W1), W98–W102 (2017).
  • Song Y , ZhengS , WangJet al. Hypoxia-induced PLOD2 promotes proliferation, migration and invasion via PI3K/Akt signaling in glioma. Oncotarget8(26), 41947–41962 (2017).
  • Wang L , PengZ , WangKet al. NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1. PeerJ5, e4065 (2017).
  • Wang T , Abou-OufH , HegazySAet al. Ankyrin G expression is associated with androgen receptor stability, invasiveness, and lethal outcome in prostate cancer patients. J. Mol. Med.94(12), 1411–1422 (2016).
  • Kurozumi S , JosephC , RaafatSet al. Utility of ankyrin 3 as a prognostic marker in androgen-receptor-positive breast cancer. Breast Cancer Res. Treat.176(1), 63–73 (2019).
  • Zhou L , FuL , LvNet al. Methylation-associated silencing of BASP1 contributes to leukemogenesis in t(8;21) acute myeloid leukemia. Exp. Mol. Med.50(4), 44 (2018).
  • Tang H , WangY , ZhangBet al. High brain acid soluble protein 1(BASP1) is a poor prognostic factor for cervical cancer and promotes tumor growth. Cancer Cell Int.17, 97 (2017).
  • Schwartz S , MumbachMR , JovanovicMet al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Rep.8(1), 284–296 (2014).
  • Luo GZ , MacqueenA , ZhengGet al. Unique features of the m6A methylome in Arabidopsis thaliana. Nat. Commun.5, 5630 (2014).

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